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Items: 1 to 20 of 48

1.

Transient reduction of DNA methylation at the onset of meiosis in male mice.

Gaysinskaya V, Miller BF, De Luca C, van der Heijden GW, Hansen KD, Bortvin A.

Epigenetics Chromatin. 2018 Apr 4;11(1):15. doi: 10.1186/s13072-018-0186-0.

2.

Improving Metabolic Health Through Precision Dietetics in Mice.

Barrington WT, Wulfridge P, Wells AE, Rojas CM, Howe SYF, Perry A, Hua K, Pellizzon MA, Hansen KD, Voy BH, Bennett BJ, Pomp D, Feinberg AP, Threadgill DW.

Genetics. 2018 Jan;208(1):399-417. doi: 10.1534/genetics.117.300536. Epub 2017 Nov 20.

3.

Software for the Integration of Multiomics Experiments in Bioconductor.

Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L.

Cancer Res. 2017 Nov 1;77(21):e39-e42. doi: 10.1158/0008-5472.CAN-17-0344.

4.

Reproducible RNA-seq analysis using recount2.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT.

Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. No abstract available.

PMID:
28398307
5.

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.

Zheng SC, Beck S, Jaffe AE, Koestler DC, Hansen KD, Houseman AE, Irizarry RA, Teschendorff AE.

Nat Methods. 2017 Feb 28;14(3):216-217. doi: 10.1038/nmeth.4187. No abstract available.

PMID:
28245219
6.

Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics.

Myint L, Kleensang A, Zhao L, Hartung T, Hansen KD.

Anal Chem. 2017 Mar 21;89(6):3517-3523. doi: 10.1021/acs.analchem.6b04719. Epub 2017 Mar 7.

7.

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA III, Karbhari N, Hansen KD, Langmead B, Leek JT.

Genome Biol. 2016 Dec 30;17(1):266. doi: 10.1186/s13059-016-1118-6.

8.

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.

Fortin JP, Triche TJ Jr, Hansen KD.

Bioinformatics. 2017 Feb 15;33(4):558-560. doi: 10.1093/bioinformatics/btw691.

9.

A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome.

Benjamin JS, Pilarowski GO, Carosso GA, Zhang L, Huso DL, Goff LA, Vernon HJ, Hansen KD, Bjornsson HT.

Proc Natl Acad Sci U S A. 2017 Jan 3;114(1):125-130. doi: 10.1073/pnas.1611431114. Epub 2016 Dec 20.

10.

"Gap hunting" to characterize clustered probe signals in Illumina methylation array data.

Andrews SV, Ladd-Acosta C, Feinberg AP, Hansen KD, Fallin MD.

Epigenetics Chromatin. 2016 Dec 7;9:56. doi: 10.1186/s13072-016-0107-z. eCollection 2016.

11.

Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver.

Li X, Liu Y, Salz T, Hansen KD, Feinberg A.

Genome Res. 2016 Dec;26(12):1730-1741. Epub 2016 Oct 13.

12.

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.

Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B.

Bioinformatics. 2016 Aug 15;32(16):2551-3. doi: 10.1093/bioinformatics/btw177. Epub 2016 Apr 21.

13.

DNA methylation is stable during replication and cell cycle arrest.

Vandiver AR, Idrizi A, Rizzardi L, Feinberg AP, Hansen KD.

Sci Rep. 2015 Dec 9;5:17911. doi: 10.1038/srep17911.

14.

Testing and Validation of Computational Methods for Mass Spectrometry.

Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A.

J Proteome Res. 2016 Mar 4;15(3):809-14. doi: 10.1021/acs.jproteome.5b00852. Epub 2015 Nov 17.

15.

Public data and open source tools for multi-assay genomic investigation of disease.

Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L.

Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12. Review.

16.

Bacterial infection remodels the DNA methylation landscape of human dendritic cells.

Pacis A, Tailleux L, Morin AM, Lambourne J, MacIsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Pastinen T, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB.

Genome Res. 2015 Dec;25(12):1801-11. doi: 10.1101/gr.192005.115. Epub 2015 Sep 21.

17.

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.

Fortin JP, Hansen KD.

Genome Biol. 2015 Aug 28;16:180. doi: 10.1186/s13059-015-0741-y.

18.

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

Vandiver AR, Irizarry RA, Hansen KD, Garza LA, Runarsson A, Li X, Chien AL, Wang TS, Leung SG, Kang S, Feinberg AP.

Genome Biol. 2015 Apr 16;16:80. doi: 10.1186/s13059-015-0644-y.

19.

Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children.

Hong X, Hao K, Ladd-Acosta C, Hansen KD, Tsai HJ, Liu X, Xu X, Thornton TA, Caruso D, Keet CA, Sun Y, Wang G, Luo W, Kumar R, Fuleihan R, Singh AM, Kim JS, Story RE, Gupta RS, Gao P, Chen Z, Walker SO, Bartell TR, Beaty TH, Fallin MD, Schleimer R, Holt PG, Nadeau KC, Wood RA, Pongracic JA, Weeks DE, Wang X.

Nat Commun. 2015 Feb 24;6:6304. doi: 10.1038/ncomms7304.

20.

Orchestrating high-throughput genomic analysis with Bioconductor.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.

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